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- PDB-8qnu: Metarhizium robertsii Woronin body major protein (HEX-1) -

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Basic information

Entry
Database: PDB / ID: 8qnu
TitleMetarhizium robertsii Woronin body major protein (HEX-1)
ComponentsWoronin body major protein
KeywordsSTRUCTURAL PROTEIN / self-assembly / natively crystallizing / HEX-1 / Woronin Body Major Protein
Function / homology
Function and homology information


positive regulation of translational elongation / translation elongation factor activity / ribosome binding / RNA binding
Similarity search - Function
Hex1, S1 domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor IF5A-like / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Woronin body major protein
Similarity search - Component
Biological speciesMetarhizium robertsii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsBoger, J. / Redecke, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K18FLA Germany
CitationJournal: To Be Published
Title: Comparison of different HEX-1 proteins
Authors: Boger, J. / Redecke, L.
History
DepositionSep 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Woronin body major protein


Theoretical massNumber of molelcules
Total (without water)23,3051
Polymers23,3051
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8760 Å2
Unit cell
Length a, b, c (Å)57.650, 57.650, 198.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Woronin body major protein


Mass: 23305.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metarhizium robertsii (fungus) / Gene: MAA_00782 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: E9EN82
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 300 K / Method: in cell
Details: MrHEX-1 crystallized spontaneously in living T. ni High Five cells after recombinant expression using the baculovirus expression system (DH10EmBacY)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.72→66.1 Å / Num. obs: 21819 / % possible obs: 99.8 % / Redundancy: 880.6 % / Biso Wilson estimate: 28.05 Å2 / CC1/2: 0.9988 / Net I/σ(I): 21.92
Reflection shellResolution: 1.72→1.73 Å / Num. unique obs: 1065 / CC1/2: 0.2594
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→49.93 Å / SU ML: 0.205 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2241 3026 7.75 %
Rwork0.192 36020 -
obs0.1945 21620 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.05 Å2
Refinement stepCycle: LAST / Resolution: 1.72→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 0 93 1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571177
X-RAY DIFFRACTIONf_angle_d0.83921593
X-RAY DIFFRACTIONf_chiral_restr0.06185
X-RAY DIFFRACTIONf_plane_restr0.0056202
X-RAY DIFFRACTIONf_dihedral_angle_d5.2625159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.750.38251340.39611564X-RAY DIFFRACTION94.7
1.75-1.780.33871340.33671605X-RAY DIFFRACTION99.31
1.78-1.810.3421380.28481651X-RAY DIFFRACTION99.89
1.81-1.840.24941390.25511633X-RAY DIFFRACTION100
1.84-1.870.27871330.22621650X-RAY DIFFRACTION100
1.87-1.910.23061330.21041638X-RAY DIFFRACTION100
1.91-1.950.22141400.20531653X-RAY DIFFRACTION100
1.95-20.21051390.18491649X-RAY DIFFRACTION99.94
2-2.050.16921400.18251609X-RAY DIFFRACTION100
2.05-2.110.21821390.18811643X-RAY DIFFRACTION99.94
2.11-2.170.23881390.18291640X-RAY DIFFRACTION100
2.17-2.240.22371380.18231653X-RAY DIFFRACTION100
2.24-2.320.2171380.18681660X-RAY DIFFRACTION99.94
2.32-2.410.23761410.18141625X-RAY DIFFRACTION100
2.41-2.520.24511360.19831642X-RAY DIFFRACTION100
2.52-2.650.26611370.20351625X-RAY DIFFRACTION100
2.65-2.820.27521390.19591649X-RAY DIFFRACTION100
2.82-3.040.22711410.20591657X-RAY DIFFRACTION100
3.04-3.340.22681340.20131644X-RAY DIFFRACTION100
3.34-3.820.2221400.17471645X-RAY DIFFRACTION100
3.83-4.810.18741310.1481643X-RAY DIFFRACTION100
4.82-49.930.19941430.20171642X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.909423940391.805114399383.595505369582.132971124870.3569287677457.94084601920.0646777024969-0.243912472792-0.250056930134-0.08065116876120.286342380808-0.250917306737-1.12308999845-0.342064195155-0.2852449077010.8369188274880.181161268460.0254897860080.5430224460840.03319483841530.79803771623632.648168818842.66328611150.3950988295
23.742262127261.203560135712.253819726471.835553805920.3377894895372.49031241848-0.0890497442394-0.07032716156050.1741582438220.0955056181164-0.114408453107-0.0336854390424-0.1954100678850.1449079990540.2030769955810.158105554956-0.02878977178150.003477318008490.1694958755060.001456435017640.14980422925834.058633202328.564438485239.8333770411
36.37210023242-2.458237405811.31083486587.48203129310.6118299772373.59306090762-0.168275843574-0.19031002916-0.1933931886040.1997296758290.1319486622030.01442965538650.07015656541350.03682572619630.05131617279910.160060867540.006733181434220.01447548275430.2136265592240.006968589756720.1992186766118.8374147428127.307786023736.5612083015
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 31 )1 - 311 - 9
22chain 'A' and (resid 32 through 103 )32 - 10310 - 81
33chain 'A' and (resid 104 through 172 )104 - 17282 - 150

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